Getting Started with Bonsai
Bonsai is an open source software capable of processing many heterogeneous streams of data in parallel; it is also our software of choice for running fiber photometry experiments using a Neurophotometrics system.
Gonçalo Lopes founded Bonsai as a free yet efficient method to track an animal’s behaviour during graduate school at the Champalimaud Centre for the Unknown. We work closely with Gonçalo to improve the way scientists acquire and analyze data. As an open source software, Bonsai is free to use and not proprietary to any one company; therefore, you can use Bonsai to acquire from or run many behavioural paradigms. The entire program is made in C#, but because it is designed for scientists, the user interface has deviated from utilizing syntactical devices used by other coding languages that many find annoying if they aren’t already fluent coders. Instead, Bonsai is a visual coding language, and its user interface relies on understanding a flow of logic and connecting nodes to achieve your desired outcome.
At Neurophotometrics, we specifically like using Bonsai to timelock photometry data to events in other domains, including operant tasks, EEG, elevated mazes, forced swim tests, audio analysis, and more. Bonsai has many built-in nodes for analyzing such data, but its flexibility extends farther than connecting pre-existing nodes; you can output Python commands if Bonsai’s built in nodes are not sufficient. Furthermore, you can contribute to the community by developing your own packages if you are familiar with C#.
While documentation is limited, Gonçalo moderates a Bonsai Google forum where questions can be posted and code can be shared. In addition, scientists at Neurophotometrics can be called upon as a resource to help timelock photometry data to your behavioural events.It all begins with an idea. Maybe you want to launch a business. Maybe you want to turn a hobby into something more. Or maybe you have a creative project to share with the world. Whatever it is, the way you tell your story online can make all the difference.
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